Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection DOI Creative Commons
Xuelei Lin, Yongxin Xu, Dongzhi Wang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Nov. 11, 2022

Abstract The spike architecture of wheat plays a crucial role in determining grain number, making it key trait to optimize breeding programs. In this study, through multi-omic approach, we analyzed the transcriptome and epigenome profiles shoot apex at eight developmental stages, revealing coordinated changes chromatin accessibility H3K27me3 abundance during flowering transition. We constructed core transcriptional regulatory network (TRN) that drives formation, experimentally validated multi-layer module involving TaSPL15, TaAGLG1, TaFUL2. By integrating TRN with genome-wide association analysis (GWAS), identified 227 transcription factors (TFs), including 42 known functions 185 unknown functions. Further investigation 61 novel TFs using multiple homozygous mutant lines uncovered 36 altered or time, such as TaMYC2-A1, TaMYB30-A1, TaWRKY37-A1. Of particular interest, downstream repressed by WFZP, was found regulate fertile spikelet number. Notably, domestication process China, excellent haplotype TaMYB30-A1 containing C allele WFZP binding site enriched, leading improved agronomic traits. Our study presents high-confidence regulators offers an effective strategy for understanding genetic basis development, practical impact applications.

Language: Английский

Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement DOI Creative Commons
Hude Mao, Cong Jiang, Chunlei Tang

et al.

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(10), P. 1564 - 1589

Published: Sept. 9, 2023

Language: Английский

Citations

46
Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses DOI Creative Commons
Xuelei Lin, Yongxin Xu, Dongzhi Wang

et al.

Molecular Plant, Journal Year: 2024, Volume and Issue: 17(3), P. 438 - 459

Published: Feb. 2, 2024

Language: Английский

Citations

19
Grain yield improvement by genome editing of TaARF12 that decoupled peduncle and rachis development trajectories via differential regulation of gibberellin signalling in wheat DOI Creative Commons

Xingchen Kong,

Fang Wang, Zhenyu Wang

et al.

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21(10), P. 1990 - 2001

Published: Aug. 17, 2023

Summary Plant breeding is constrained by trade‐offs among different agronomic traits the pleiotropic nature of many genes. Genes that contribute to two or more favourable with no penalty on yield are rarely reported, especially in wheat. Here, we describe editing a wheat auxin response factor TaARF12 using CRISPR/Cas9 rendered shorter plant height larger spikes. Changes architecture enhanced grain number per spike up 14.7% significantly higher thousand‐grain weight and 11.1% increase under field trials. Weighted Gene Co‐Expression Network Analysis (WGCNA) spatial–temporal transcriptome profiles revealed hub genes: RhtL1 , DELLA domain‐free Rht‐1 paralog, which was up‐regulated peduncle, TaNGR5 an organ size regulator rachis, taarf12 plants. The up‐regulation peduncle suggested repression GA signalling, whereas may promote response, working model supported differential expression patterns biogenesis genes tissues. Thus, complemented reduction spikes gave yield. Manipulation represent new strategy trait pyramiding for improvement

Language: Английский

Citations

26
Genetics aspect of vitamin C (Ascorbic Acid) biosynthesis and signaling pathways in fruits and vegetables crops DOI
Adnan Sami, Shiming Han, Muhammad Zeshan Haider

et al.

Functional & Integrative Genomics, Journal Year: 2024, Volume and Issue: 24(2)

Published: April 1, 2024

Language: Английский

Citations

11
The translational landscape of bread wheat during grain development DOI Open Access
Yiwen Guo, Yongming Chen, Yongfa Wang

et al.

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(6), P. 1848 - 1867

Published: March 11, 2023

The dynamics of gene expression in crop grains has typically been investigated at the transcriptional level. However, this approach neglects translational regulation, a widespread mechanism that rapidly modulates to increase plasticity organisms. Here, we performed ribosome profiling and polysome obtain comprehensive translatome data set developing bread wheat (Triticum aestivum) grains. We further genome-wide during grain development, revealing translation many functional genes is modulated stage-specific manner. unbalanced between subgenomes pervasive, which increases flexibility allohexaploid wheat. In addition, uncovered previously unannotated events, including upstream open reading frames (uORFs), downstream (dORFs), (ORFs) long noncoding RNAs, characterized temporal small ORFs. demonstrated uORFs act as cis-regulatory elements can repress or even enhance mRNAs. Gene may be combinatorially by uORFs, dORFs, microRNAs. summary, our study presents translatomic resource provides detailed overview regulation This will facilitate future improvements for optimal yield quality.

Language: Английский

Citations

19
Deciphering the evolution and complexity of wheat germplasm from a genomic perspective DOI Creative Commons
Zihao Wang, Ling-Feng Miao, Yongming Chen

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2023, Volume and Issue: 50(11), P. 846 - 860

Published: Aug. 21, 2023

Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progresses in studying on genome are substantially trailed behind those other two major crops, rice maize, at least a decade. With rapid advances assembling reduced cost high-throughput sequencing, emerging de novo assemblies whole-genome sequencing data leading paradigm shift research. Here, we review recent progress dissecting germplasm evolution since release first high-quality genome. New insights have been gained during domestication modern breeding progress, genomic variations multiple scales contributing diversity germplasm, transcriptional epigenetic regulations functional genes polyploid wheat. Genomics databases bioinformatics tools meeting urgent needs genomics research also summarized. The ever-increasing omics data, along with advanced well-structured databases, expected accelerate deciphering gene resources future advances.

Language: Английский

Citations

14
Innovative computational tools provide new insights into the polyploid wheat genome DOI Creative Commons
Yongming Chen, Wenxi Wang, Zhengzhao Yang

et al.

aBIOTECH, Journal Year: 2024, Volume and Issue: 5(1), P. 52 - 70

Published: Feb. 7, 2024

Abstract Bread wheat ( Triticum aestivum ) is an important crop and serves as a significant source of protein calories for humans, worldwide. Nevertheless, its large allopolyploid genome poses constraints on genetic improvement. The complex reticulate evolutionary history the intricacy genomic resources make deciphering functional considerably more challenging. Recently, we have developed comprehensive list versatile computational tools with integration statistical models dissecting polyploid genome. Here, summarize methodological innovations applications these databases. A series step-by-step examples illustrates how can be utilized germplasm unveiling genes associated agronomic traits. Furthermore, outline future perspectives new advanced databases, taking into consideration unique features bread wheat, to accelerate genomic-assisted breeding.

Language: Английский

Citations

6
Reshaped DNA methylation cooperating with homoeolog‐divergent expression promotes improved root traits in synthesized tetraploid wheat DOI Creative Commons
Ling-Feng Miao, Weiya Xu, Yanhong Liu

et al.

New Phytologist, Journal Year: 2024, Volume and Issue: 242(2), P. 507 - 523

Published: Feb. 16, 2024

Polyploidization is a major event driving plant evolution and domestication. However, how reshaped epigenetic modifications coordinate gene transcription to generate phenotypic variations during wheat polyploidization currently elusive. Here, we profiled transcriptomes DNA methylomes of two diploid accessions (S

Language: Английский

Citations

6
CRISPR‐targeted mutagenesis of mitogen‐activated protein kinase phosphatase 1 improves both immunity and yield in wheat DOI Creative Commons
Saifei Liu, Fengfeng Zhang,

Jiaxuan Su

et al.

Plant Biotechnology Journal, Journal Year: 2024, Volume and Issue: 22(7), P. 1929 - 1941

Published: Feb. 16, 2024

Summary Plants have evolved a sophisticated immunity system for specific detection of pathogens and rapid induction measured defences. Over‐ or constitutive activation defences would negatively affect plant growth development. Hence, the immune is under tight positive negative regulation. MAP kinase phosphatase1 (MKP1) has been identified as regulator in model Arabidopsis . However, molecular mechanisms by which MKP1 regulates signalling wheat ( Triticum aestivum ) are poorly understood. In this study, we investigated role TaMKP1 defence against two devastating fungal determined its subcellular localization. We demonstrated that knock‐down CRISPR/Cas9 resulted enhanced resistance to rust caused Puccinia striiformis f. sp. tritici Pst powdery mildew Blumeria graminis Bgt ), indicating disease wheat. Unexpectedly, while Tamkp1 mutant plants showed increased tested they also had higher yield compared with wild‐type control without infection. Our results suggested interacts directly dephosphorylated activated TaMPK3/4/6, TaMPK4 TaPAL. Taken together, exert modulating roles required MAPK‐mediated signalling. This facilitates our understanding important phosphatases MAPK cascades production, provides germplasm resources breeding high yield.

Language: Английский

Citations

6
Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat DOI Creative Commons
Ai Guo, Chao He,

Siteng Bi

et al.

Plant Communications, Journal Year: 2024, Volume and Issue: 5(5), P. 100879 - 100879

Published: March 14, 2024

Spike architecture influences both grain weight and number per spike, which are the two major components of yield in bread wheat (Triticum aestivum L.). However, complex genome influence various environmental factors pose challenges mapping causal genes that affect spike traits. Here, we systematically identified involved trait formation by integrating information on genomic variation gene regulatory networks controlling young development wheat. We 170 loci responsible for variations length, spikelet through genome-wide association study meta-QTL analyses. constructed inflorescences at double ridge stage floret primordium stage, meristem predominant, respectively, transcriptome, histone modification, chromatin accessibility, eQTL, protein-protein interactome data. From these networks, 169 hub located 76 QTL regions whose polymorphisms significantly associated with The functions TaZF-B1, VRT-B2, TaSPL15-A/D establishment were verified. This provides valuable molecular resources understanding traits demonstrates combining genetic analysis developmental is a robust approach dissection

Language: Английский

Citations

6